Starting phenix.real_space_refine on Mon Jun 23 03:46:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t3i_25659/06_2025/7t3i_25659.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3i_25659/06_2025/7t3i_25659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t3i_25659/06_2025/7t3i_25659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3i_25659/06_2025/7t3i_25659.map" model { file = "/net/cci-nas-00/data/ceres_data/7t3i_25659/06_2025/7t3i_25659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3i_25659/06_2025/7t3i_25659.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 25 5.49 5 S 123 5.16 5 C 16704 2.51 5 N 4786 2.21 5 O 5161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26799 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4437 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 545} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 4443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4443 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4433 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 4443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4443 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 4412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4412 Classifications: {'peptide': 574} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 542} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 4243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4243 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 523} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 135 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'ATP': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.64, per 1000 atoms: 0.66 Number of scatterers: 26799 At special positions: 0 Unit cell: (151.152, 145.904, 117.563, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 123 16.00 P 25 15.00 O 5161 8.00 N 4786 7.00 C 16704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.04 Conformation dependent library (CDL) restraints added in 3.6 seconds 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6432 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 12 sheets defined 59.9% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.987A pdb=" N LYS A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 278 through 294 Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.937A pdb=" N ILE A 322 " --> pdb=" O MET A 318 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 363 removed outlier: 4.286A pdb=" N ARG A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 407 through 438 removed outlier: 4.139A pdb=" N ALA A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 460 removed outlier: 3.723A pdb=" N HIS A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.606A pdb=" N SER A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 517 through 523 removed outlier: 3.596A pdb=" N ILE A 521 " --> pdb=" O ILE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.778A pdb=" N PHE A 527 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.646A pdb=" N LYS A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 593 removed outlier: 3.759A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 606 Processing helix chain 'A' and resid 618 through 632 Processing helix chain 'A' and resid 670 through 684 removed outlier: 3.865A pdb=" N VAL A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 717 No H-bonds generated for 'chain 'A' and resid 715 through 717' Processing helix chain 'A' and resid 718 through 724 Processing helix chain 'A' and resid 725 through 729 removed outlier: 3.760A pdb=" N THR A 729 " --> pdb=" O LEU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 776 through 786 removed outlier: 4.045A pdb=" N TRP A 780 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 781 " --> pdb=" O MET A 777 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 786 " --> pdb=" O LYS A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 799 removed outlier: 3.854A pdb=" N TYR A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 207 through 224 removed outlier: 4.740A pdb=" N PHE B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 248 through 261 removed outlier: 3.628A pdb=" N HIS B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.873A pdb=" N VAL B 272 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 273 " --> pdb=" O PRO B 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 269 through 273' Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 303 through 308 removed outlier: 4.315A pdb=" N ILE B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 337 removed outlier: 3.866A pdb=" N ASP B 331 " --> pdb=" O MET B 327 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 363 removed outlier: 3.776A pdb=" N ARG B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 363 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.506A pdb=" N MET B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 438 removed outlier: 4.529A pdb=" N ALA B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASN B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 removed outlier: 3.535A pdb=" N ALA B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 483 removed outlier: 3.568A pdb=" N SER B 481 " --> pdb=" O ARG B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 517 through 523 Processing helix chain 'B' and resid 523 through 531 removed outlier: 3.554A pdb=" N PHE B 527 " --> pdb=" O ASN B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 560 removed outlier: 3.871A pdb=" N LYS B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 593 removed outlier: 3.664A pdb=" N SER B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU B 580 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 581 " --> pdb=" O GLY B 577 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.840A pdb=" N LEU B 606 " --> pdb=" O GLN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 631 removed outlier: 3.511A pdb=" N ARG B 620 " --> pdb=" O ASP B 616 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 650 removed outlier: 3.665A pdb=" N ILE B 650 " --> pdb=" O PRO B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 684 removed outlier: 4.099A pdb=" N VAL B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 724 Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 732 through 762 removed outlier: 3.510A pdb=" N GLY B 737 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 761 " --> pdb=" O GLN B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 785 removed outlier: 3.917A pdb=" N TRP B 780 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 798 Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 207 through 224 removed outlier: 3.661A pdb=" N LYS C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Proline residue: C 221 - end of helix Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 248 through 261 Processing helix chain 'C' and resid 270 through 273 Processing helix chain 'C' and resid 278 through 294 Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'C' and resid 316 through 337 removed outlier: 3.731A pdb=" N SER C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 321 " --> pdb=" O GLY C 317 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 322 " --> pdb=" O MET C 318 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP C 331 " --> pdb=" O MET C 327 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR C 337 " --> pdb=" O ILE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.590A pdb=" N PHE C 354 " --> pdb=" O ARG C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 363 removed outlier: 3.560A pdb=" N ARG C 362 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 363 " --> pdb=" O ILE C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.861A pdb=" N LEU C 399 " --> pdb=" O ASN C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 438 removed outlier: 4.027A pdb=" N ALA C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN C 426 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 428 " --> pdb=" O GLN C 424 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 430 " --> pdb=" O ASN C 426 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 460 Processing helix chain 'C' and resid 472 through 481 removed outlier: 3.525A pdb=" N PHE C 476 " --> pdb=" O THR C 472 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 491 removed outlier: 3.572A pdb=" N GLU C 490 " --> pdb=" O SER C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 503 Processing helix chain 'C' and resid 506 through 517 Processing helix chain 'C' and resid 517 through 523 Processing helix chain 'C' and resid 523 through 531 removed outlier: 3.560A pdb=" N PHE C 527 " --> pdb=" O ASN C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 560 removed outlier: 3.959A pdb=" N LYS C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 593 removed outlier: 3.764A pdb=" N SER C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU C 580 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 583 " --> pdb=" O SER C 579 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 592 " --> pdb=" O SER C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 631 Processing helix chain 'C' and resid 670 through 686 removed outlier: 4.091A pdb=" N VAL C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS C 676 " --> pdb=" O GLU C 672 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C 685 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 724 Processing helix chain 'C' and resid 725 through 729 removed outlier: 3.717A pdb=" N THR C 729 " --> pdb=" O LEU C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 762 removed outlier: 3.828A pdb=" N GLY C 737 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 785 Processing helix chain 'C' and resid 794 through 799 removed outlier: 3.908A pdb=" N HIS C 799 " --> pdb=" O GLU C 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 207 through 224 removed outlier: 4.042A pdb=" N LYS D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.547A pdb=" N CYS D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 261 removed outlier: 3.593A pdb=" N HIS D 254 " --> pdb=" O THR D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.884A pdb=" N VAL D 272 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 294 Processing helix chain 'D' and resid 303 through 308 removed outlier: 3.943A pdb=" N ILE D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 337 removed outlier: 4.162A pdb=" N SER D 320 " --> pdb=" O LYS D 316 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP D 331 " --> pdb=" O MET D 327 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 332 " --> pdb=" O ASN D 328 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.809A pdb=" N ARG D 361 " --> pdb=" O PRO D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.746A pdb=" N GLN D 379 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 380 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 381 " --> pdb=" O ARG D 377 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 402 removed outlier: 4.151A pdb=" N LEU D 399 " --> pdb=" O ASN D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 438 removed outlier: 4.130A pdb=" N ALA D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN D 426 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 460 removed outlier: 3.635A pdb=" N HIS D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.743A pdb=" N SER D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 506 through 517 Processing helix chain 'D' and resid 517 through 523 Processing helix chain 'D' and resid 523 through 531 removed outlier: 3.569A pdb=" N PHE D 527 " --> pdb=" O ASN D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 560 removed outlier: 3.504A pdb=" N LYS D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 593 removed outlier: 3.899A pdb=" N SER D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU D 580 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 583 " --> pdb=" O SER D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 607 removed outlier: 4.132A pdb=" N LEU D 606 " --> pdb=" O GLN D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 631 removed outlier: 4.100A pdb=" N ARG D 620 " --> pdb=" O ASP D 616 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL D 621 " --> pdb=" O ALA D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 650 removed outlier: 3.854A pdb=" N ILE D 650 " --> pdb=" O PRO D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 684 removed outlier: 3.876A pdb=" N VAL D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS D 676 " --> pdb=" O GLU D 672 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN D 684 " --> pdb=" O THR D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 724 Processing helix chain 'D' and resid 725 through 729 Processing helix chain 'D' and resid 732 through 762 removed outlier: 3.720A pdb=" N GLY D 737 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS D 758 " --> pdb=" O GLN D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 776 through 784 removed outlier: 3.566A pdb=" N TRP D 780 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 797 Processing helix chain 'E' and resid 200 through 204 Processing helix chain 'E' and resid 207 through 218 removed outlier: 3.884A pdb=" N ARG E 213 " --> pdb=" O ASP E 209 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 224 removed outlier: 3.520A pdb=" N ARG E 223 " --> pdb=" O TRP E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 248 through 261 Processing helix chain 'E' and resid 270 through 273 Processing helix chain 'E' and resid 279 through 294 Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 316 through 336 removed outlier: 3.994A pdb=" N SER E 320 " --> pdb=" O LYS E 316 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 356 through 363 removed outlier: 3.783A pdb=" N PHE E 363 " --> pdb=" O ILE E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 407 through 438 removed outlier: 3.779A pdb=" N ALA E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN E 426 " --> pdb=" O SER E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 460 removed outlier: 3.508A pdb=" N LEU E 455 " --> pdb=" O ARG E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 479 removed outlier: 3.783A pdb=" N PHE E 476 " --> pdb=" O THR E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 503 Processing helix chain 'E' and resid 506 through 517 Processing helix chain 'E' and resid 517 through 523 Processing helix chain 'E' and resid 523 through 531 removed outlier: 3.603A pdb=" N VAL E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 560 Processing helix chain 'E' and resid 568 through 572 removed outlier: 4.464A pdb=" N LEU E 571 " --> pdb=" O GLY E 568 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 572 " --> pdb=" O PRO E 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 568 through 572' Processing helix chain 'E' and resid 577 through 593 removed outlier: 3.538A pdb=" N ALA E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL E 583 " --> pdb=" O SER E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 606 Processing helix chain 'E' and resid 616 through 632 removed outlier: 3.590A pdb=" N VAL E 621 " --> pdb=" O ALA E 617 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR E 624 " --> pdb=" O ARG E 620 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL E 632 " --> pdb=" O GLU E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 650 Processing helix chain 'E' and resid 672 through 684 removed outlier: 4.469A pdb=" N LYS E 676 " --> pdb=" O GLU E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 715 through 724 removed outlier: 3.711A pdb=" N LEU E 719 " --> pdb=" O THR E 715 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU E 720 " --> pdb=" O ASP E 716 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 756 removed outlier: 3.529A pdb=" N GLN E 756 " --> pdb=" O TYR E 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 776 through 786 removed outlier: 3.825A pdb=" N TRP E 780 " --> pdb=" O THR E 776 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 204 Processing helix chain 'F' and resid 207 through 223 removed outlier: 4.597A pdb=" N LYS F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU F 217 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N PHE F 220 " --> pdb=" O LYS F 216 " (cutoff:3.500A) Proline residue: F 221 - end of helix Processing helix chain 'F' and resid 224 through 232 removed outlier: 4.352A pdb=" N CYS F 228 " --> pdb=" O GLY F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 261 removed outlier: 3.810A pdb=" N GLY F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 294 Processing helix chain 'F' and resid 304 through 308 Processing helix chain 'F' and resid 319 through 337 Processing helix chain 'F' and resid 351 through 355 Processing helix chain 'F' and resid 356 through 363 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 402 removed outlier: 3.947A pdb=" N LEU F 399 " --> pdb=" O ASN F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 438 removed outlier: 3.504A pdb=" N ALA F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN F 426 " --> pdb=" O SER F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 460 removed outlier: 3.579A pdb=" N HIS F 459 " --> pdb=" O LEU F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 483 removed outlier: 3.698A pdb=" N SER F 481 " --> pdb=" O ARG F 477 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 482 " --> pdb=" O LYS F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 517 Processing helix chain 'F' and resid 517 through 523 Processing helix chain 'F' and resid 523 through 531 removed outlier: 3.807A pdb=" N PHE F 527 " --> pdb=" O ASN F 523 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR F 528 " --> pdb=" O PRO F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 560 Processing helix chain 'F' and resid 576 through 593 removed outlier: 4.235A pdb=" N GLU F 580 " --> pdb=" O VAL F 576 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG F 581 " --> pdb=" O GLY F 577 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 583 " --> pdb=" O SER F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 602 through 606 Processing helix chain 'F' and resid 615 through 632 removed outlier: 3.686A pdb=" N VAL F 632 " --> pdb=" O GLU F 628 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 650 removed outlier: 3.603A pdb=" N MET F 649 " --> pdb=" O ARG F 646 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE F 650 " --> pdb=" O PRO F 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 646 through 650' Processing helix chain 'F' and resid 651 through 656 removed outlier: 4.134A pdb=" N ARG F 655 " --> pdb=" O ASP F 651 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG F 656 " --> pdb=" O GLU F 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 651 through 656' Processing helix chain 'F' and resid 670 through 685 removed outlier: 3.502A pdb=" N LYS F 676 " --> pdb=" O GLU F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 715 through 724 Processing helix chain 'F' and resid 732 through 761 removed outlier: 4.101A pdb=" N GLY F 737 " --> pdb=" O GLY F 733 " (cutoff:3.500A) Processing helix chain 'F' and resid 776 through 787 Processing sheet with id=AA1, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.775A pdb=" N ALA A 263 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N PHE A 300 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE A 265 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASP A 302 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL A 267 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS A 297 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU A 346 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE A 299 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA A 348 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 301 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY A 238 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE A 367 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 240 " --> pdb=" O ILE A 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 562 through 567 removed outlier: 3.501A pdb=" N ASP A 601 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 643 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ILE A 664 " --> pdb=" O GLY A 537 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 539 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 263 through 267 removed outlier: 3.557A pdb=" N PHE B 300 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS B 297 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU B 346 " --> pdb=" O CYS B 297 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE B 299 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ALA B 348 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU B 301 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 562 through 566 removed outlier: 3.565A pdb=" N ASP B 601 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 643 " --> pdb=" O PHE B 600 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR B 662 " --> pdb=" O GLY B 537 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 539 " --> pdb=" O THR B 662 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 268 removed outlier: 3.614A pdb=" N PHE C 300 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP C 302 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N CYS C 297 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU C 346 " --> pdb=" O CYS C 297 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE C 299 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA C 348 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 301 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY C 238 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE C 367 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU C 240 " --> pdb=" O ILE C 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 562 through 567 removed outlier: 6.820A pdb=" N ASN C 562 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE C 599 " --> pdb=" O ASN C 562 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE C 564 " --> pdb=" O PHE C 599 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASP C 601 " --> pdb=" O ILE C 564 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 566 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR C 662 " --> pdb=" O GLY C 537 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 263 through 267 removed outlier: 4.010A pdb=" N PHE D 300 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS D 297 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU D 346 " --> pdb=" O CYS D 297 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE D 299 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA D 348 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU D 301 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL D 365 " --> pdb=" O GLY D 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 562 through 567 removed outlier: 7.247A pdb=" N ASN D 562 " --> pdb=" O ILE D 597 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N PHE D 599 " --> pdb=" O ASN D 562 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE D 564 " --> pdb=" O PHE D 599 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASP D 601 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE D 566 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 538 " --> pdb=" O VAL D 640 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY D 537 " --> pdb=" O THR D 662 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE D 664 " --> pdb=" O GLY D 537 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU D 539 " --> pdb=" O ILE D 664 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.825A pdb=" N ALA E 263 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N PHE E 300 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE E 265 " --> pdb=" O PHE E 300 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP E 302 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL E 267 " --> pdb=" O ASP E 302 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS E 297 " --> pdb=" O VAL E 344 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU E 346 " --> pdb=" O CYS E 297 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE E 299 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA E 348 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU E 301 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 349 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL E 365 " --> pdb=" O GLY E 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 562 through 565 removed outlier: 7.014A pdb=" N ILE E 538 " --> pdb=" O GLY E 642 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR E 662 " --> pdb=" O GLY E 537 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 264 through 267 removed outlier: 6.504A pdb=" N ILE F 265 " --> pdb=" O PHE F 300 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASP F 302 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL F 267 " --> pdb=" O ASP F 302 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N CYS F 297 " --> pdb=" O VAL F 344 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LEU F 346 " --> pdb=" O CYS F 297 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE F 299 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ALA F 348 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU F 301 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL F 239 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR F 349 " --> pdb=" O VAL F 239 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU F 241 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 365 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS F 242 " --> pdb=" O ILE F 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 562 through 566 removed outlier: 6.048A pdb=" N ASN F 562 " --> pdb=" O ILE F 597 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE F 599 " --> pdb=" O ASN F 562 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE F 564 " --> pdb=" O PHE F 599 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS F 596 " --> pdb=" O TYR F 639 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE F 641 " --> pdb=" O CYS F 596 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU F 598 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA F 643 " --> pdb=" O LEU F 598 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE F 600 " --> pdb=" O ALA F 643 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE F 538 " --> pdb=" O GLY F 642 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ILE F 664 " --> pdb=" O GLY F 537 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU F 539 " --> pdb=" O ILE F 664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 1308 hydrogen bonds defined for protein. 3753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.10 Time building geometry restraints manager: 8.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9127 1.34 - 1.46: 5386 1.46 - 1.58: 12492 1.58 - 1.70: 32 1.70 - 1.82: 205 Bond restraints: 27242 Sorted by residual: bond pdb=" O3 PO4 E 901 " pdb=" P PO4 E 901 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.81e+00 bond pdb=" O4 PO4 E 901 " pdb=" P PO4 E 901 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.60e+00 bond pdb=" O2 PO4 E 901 " pdb=" P PO4 E 901 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.46e+00 bond pdb=" O1 PO4 E 901 " pdb=" P PO4 E 901 " ideal model delta sigma weight residual 1.565 1.510 0.055 2.00e-02 2.50e+03 7.59e+00 bond pdb=" CB PRO B 270 " pdb=" CG PRO B 270 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.05e+00 ... (remaining 27237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 36495 2.40 - 4.81: 371 4.81 - 7.21: 27 7.21 - 9.61: 4 9.61 - 12.01: 3 Bond angle restraints: 36900 Sorted by residual: angle pdb=" CA LEU C 660 " pdb=" CB LEU C 660 " pdb=" CG LEU C 660 " ideal model delta sigma weight residual 116.30 128.31 -12.01 3.50e+00 8.16e-02 1.18e+01 angle pdb=" CA PRO B 270 " pdb=" N PRO B 270 " pdb=" CD PRO B 270 " ideal model delta sigma weight residual 112.00 107.46 4.54 1.40e+00 5.10e-01 1.05e+01 angle pdb=" CG ARG B 321 " pdb=" CD ARG B 321 " pdb=" NE ARG B 321 " ideal model delta sigma weight residual 112.00 119.06 -7.06 2.20e+00 2.07e-01 1.03e+01 angle pdb=" C GLU F 217 " pdb=" N VAL F 218 " pdb=" CA VAL F 218 " ideal model delta sigma weight residual 123.16 119.86 3.30 1.06e+00 8.90e-01 9.70e+00 angle pdb=" N ILE F 654 " pdb=" CA ILE F 654 " pdb=" C ILE F 654 " ideal model delta sigma weight residual 111.90 109.41 2.49 8.10e-01 1.52e+00 9.41e+00 ... (remaining 36895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 15429 18.01 - 36.02: 1238 36.02 - 54.03: 171 54.03 - 72.04: 80 72.04 - 90.05: 24 Dihedral angle restraints: 16942 sinusoidal: 7009 harmonic: 9933 Sorted by residual: dihedral pdb=" CA GLU E 770 " pdb=" C GLU E 770 " pdb=" N ILE E 771 " pdb=" CA ILE E 771 " ideal model delta harmonic sigma weight residual 180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA THR F 494 " pdb=" C THR F 494 " pdb=" N ILE F 495 " pdb=" CA ILE F 495 " ideal model delta harmonic sigma weight residual -180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLU C 570 " pdb=" C GLU C 570 " pdb=" N LEU C 571 " pdb=" CA LEU C 571 " ideal model delta harmonic sigma weight residual -180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 16939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2880 0.036 - 0.072: 946 0.072 - 0.108: 296 0.108 - 0.144: 69 0.144 - 0.180: 5 Chirality restraints: 4196 Sorted by residual: chirality pdb=" CA GLN F 448 " pdb=" N GLN F 448 " pdb=" C GLN F 448 " pdb=" CB GLN F 448 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA GLN C 448 " pdb=" N GLN C 448 " pdb=" C GLN C 448 " pdb=" CB GLN C 448 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA VAL B 407 " pdb=" N VAL B 407 " pdb=" C VAL B 407 " pdb=" CB VAL B 407 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 4193 not shown) Planarity restraints: 4790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 484 " -0.044 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO A 485 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 485 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 485 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 484 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO C 485 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 485 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 485 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 356 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO F 357 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO F 357 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 357 " 0.029 5.00e-02 4.00e+02 ... (remaining 4787 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 446 2.66 - 3.22: 26285 3.22 - 3.78: 41214 3.78 - 4.34: 53653 4.34 - 4.90: 86222 Nonbonded interactions: 207820 Sorted by model distance: nonbonded pdb=" OG SER D 732 " pdb=" OD1 ASP D 735 " model vdw 2.101 3.040 nonbonded pdb=" OH TYR F 406 " pdb=" O VAL F 483 " model vdw 2.176 3.040 nonbonded pdb=" O TYR D 235 " pdb=" ND2 ASN D 342 " model vdw 2.187 3.120 nonbonded pdb=" OD1 ASN B 237 " pdb=" OG SER B 364 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR B 797 " pdb=" OE1 GLU C 652 " model vdw 2.219 3.040 ... (remaining 207815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 199 through 225 or (resid 226 through 230 and (name N or n \ ame CA or name C or name O or name CB )) or resid 231 through 272 or resid 277 t \ hrough 309 or resid 318 through 460 or (resid 461 through 463 and (name N or nam \ e CA or name C or name O or name CB )) or resid 464 through 686 or resid 713 thr \ ough 761 or resid 770 through 790)) selection = (chain 'B' and (resid 199 through 225 or (resid 226 through 230 and (name N or n \ ame CA or name C or name O or name CB )) or resid 231 through 272 or resid 277 t \ hrough 309 or resid 318 through 686 or resid 713 through 761 or resid 768 or res \ id 771 through 790)) selection = (chain 'C' and (resid 199 through 272 or resid 277 through 309 or resid 318 thro \ ugh 460 or (resid 461 through 463 and (name N or name CA or name C or name O or \ name CB )) or resid 464 through 686 or resid 713 through 761 or resid 768 or res \ id 771 through 790)) selection = (chain 'D' and (resid 199 through 225 or (resid 226 through 230 and (name N or n \ ame CA or name C or name O or name CB )) or resid 231 through 272 or resid 277 t \ hrough 309 or resid 318 through 686 or resid 713 through 761 or resid 768 or res \ id 771 through 790)) selection = (chain 'E' and (resid 199 through 225 or (resid 226 through 230 and (name N or n \ ame CA or name C or name O or name CB )) or resid 231 through 272 or resid 277 t \ hrough 309 or resid 318 through 686 or resid 713 through 761 or resid 768 or res \ id 771 through 790)) selection = (chain 'F' and (resid 199 through 225 or (resid 226 through 230 and (name N or n \ ame CA or name C or name O or name CB )) or resid 231 through 460 or (resid 461 \ through 463 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 4 through 761 or resid 770 through 790)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 62.290 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 27244 Z= 0.124 Angle : 0.587 12.015 36900 Z= 0.316 Chirality : 0.041 0.180 4196 Planarity : 0.004 0.067 4790 Dihedral : 13.812 90.047 10510 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.71 % Favored : 94.05 % Rotamer: Outliers : 0.07 % Allowed : 0.18 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3397 helix: 1.34 (0.13), residues: 1717 sheet: 0.05 (0.28), residues: 342 loop : -0.73 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 453 HIS 0.002 0.000 HIS A 502 PHE 0.017 0.001 PHE A 731 TYR 0.035 0.001 TYR D 752 ARG 0.012 0.000 ARG D 351 Details of bonding type rmsd hydrogen bonds : bond 0.18431 ( 1308) hydrogen bonds : angle 5.90610 ( 3753) covalent geometry : bond 0.00257 (27242) covalent geometry : angle 0.58666 (36900) Misc. bond : bond 0.00052 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 449 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LEU cc_start: 0.9157 (tp) cc_final: 0.8774 (tt) REVERT: B 546 CYS cc_start: 0.8744 (m) cc_final: 0.8208 (m) REVERT: B 585 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8365 (tm-30) REVERT: C 247 CYS cc_start: 0.8329 (m) cc_final: 0.8126 (m) REVERT: C 318 MET cc_start: 0.9066 (tmm) cc_final: 0.8713 (tmm) REVERT: C 368 ASP cc_start: 0.8666 (t70) cc_final: 0.8240 (t0) REVERT: C 369 MET cc_start: 0.8571 (ptm) cc_final: 0.8348 (ppp) REVERT: C 473 MET cc_start: 0.7722 (tpt) cc_final: 0.7407 (tpp) REVERT: C 574 LYS cc_start: 0.8903 (ptmt) cc_final: 0.8686 (ptmt) REVERT: D 204 ILE cc_start: 0.9122 (tt) cc_final: 0.8916 (pt) REVERT: D 281 GLU cc_start: 0.8927 (mp0) cc_final: 0.8467 (mp0) REVERT: D 416 LYS cc_start: 0.9044 (tppt) cc_final: 0.8426 (tppt) REVERT: D 740 MET cc_start: 0.7721 (tmm) cc_final: 0.7381 (tmm) REVERT: E 304 ILE cc_start: 0.9306 (tp) cc_final: 0.9096 (tp) REVERT: E 473 MET cc_start: 0.8619 (tpt) cc_final: 0.8332 (mmm) REVERT: E 515 MET cc_start: 0.8705 (tpp) cc_final: 0.8175 (tpp) REVERT: E 630 ASP cc_start: 0.7795 (t0) cc_final: 0.7308 (t0) REVERT: F 219 TRP cc_start: 0.5802 (t-100) cc_final: 0.5574 (t-100) REVERT: F 303 GLU cc_start: 0.6467 (mp0) cc_final: 0.5972 (mp0) REVERT: F 371 MET cc_start: 0.6999 (tmm) cc_final: 0.6638 (tmm) REVERT: F 745 GLN cc_start: 0.8713 (mt0) cc_final: 0.8310 (mt0) outliers start: 2 outliers final: 0 residues processed: 450 average time/residue: 0.3636 time to fit residues: 265.5109 Evaluate side-chains 320 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 6.9990 chunk 259 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 174 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 103 optimal weight: 0.0370 chunk 162 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 310 optimal weight: 9.9990 overall best weight: 1.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN B 426 ASN B 459 HIS ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN D 585 GLN E 438 HIS ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.099591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.078686 restraints weight = 69404.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.080782 restraints weight = 42264.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.082172 restraints weight = 29389.538| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27244 Z= 0.141 Angle : 0.570 8.473 36900 Z= 0.295 Chirality : 0.042 0.207 4196 Planarity : 0.005 0.054 4790 Dihedral : 10.150 87.341 4024 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.62 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3397 helix: 1.33 (0.12), residues: 1795 sheet: -0.07 (0.28), residues: 352 loop : -0.73 (0.19), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 219 HIS 0.004 0.001 HIS E 438 PHE 0.018 0.002 PHE D 354 TYR 0.022 0.001 TYR D 413 ARG 0.012 0.000 ARG D 351 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 1308) hydrogen bonds : angle 4.64060 ( 3753) covalent geometry : bond 0.00315 (27242) covalent geometry : angle 0.57002 (36900) Misc. bond : bond 0.00021 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASP cc_start: 0.8679 (m-30) cc_final: 0.8009 (p0) REVERT: A 522 LYS cc_start: 0.8700 (mmtp) cc_final: 0.8477 (ptmt) REVERT: A 546 CYS cc_start: 0.8832 (m) cc_final: 0.8480 (m) REVERT: A 566 ILE cc_start: 0.9663 (mm) cc_final: 0.9455 (mm) REVERT: A 728 CYS cc_start: 0.7681 (t) cc_final: 0.7438 (t) REVERT: B 240 LEU cc_start: 0.8470 (tp) cc_final: 0.7880 (tp) REVERT: B 242 HIS cc_start: 0.9061 (p90) cc_final: 0.8803 (p90) REVERT: B 327 MET cc_start: 0.8573 (tpp) cc_final: 0.8235 (tpt) REVERT: B 395 ASN cc_start: 0.9183 (t0) cc_final: 0.8944 (t0) REVERT: B 401 LYS cc_start: 0.9202 (mttt) cc_final: 0.8875 (tppt) REVERT: B 546 CYS cc_start: 0.8694 (m) cc_final: 0.8182 (m) REVERT: B 740 MET cc_start: 0.8645 (tmm) cc_final: 0.8350 (tmm) REVERT: C 318 MET cc_start: 0.8751 (tmm) cc_final: 0.8401 (tmm) REVERT: C 368 ASP cc_start: 0.8775 (t70) cc_final: 0.8407 (t0) REVERT: C 473 MET cc_start: 0.7724 (tpt) cc_final: 0.7516 (tpp) REVERT: C 493 SER cc_start: 0.9193 (m) cc_final: 0.8869 (p) REVERT: C 574 LYS cc_start: 0.8923 (ptmt) cc_final: 0.8627 (ptmt) REVERT: C 652 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7518 (mt-10) REVERT: C 741 GLN cc_start: 0.8407 (tp40) cc_final: 0.8094 (tp40) REVERT: D 204 ILE cc_start: 0.9140 (tt) cc_final: 0.8924 (pt) REVERT: D 286 ASP cc_start: 0.7877 (t70) cc_final: 0.7670 (t0) REVERT: D 416 LYS cc_start: 0.9011 (tppt) cc_final: 0.7987 (tppt) REVERT: D 466 TRP cc_start: 0.6661 (p90) cc_final: 0.6410 (p90) REVERT: D 580 GLU cc_start: 0.8853 (mp0) cc_final: 0.8572 (mp0) REVERT: D 649 MET cc_start: 0.8202 (tpt) cc_final: 0.7918 (tpp) REVERT: D 740 MET cc_start: 0.7910 (tmm) cc_final: 0.7529 (tmm) REVERT: E 235 TYR cc_start: 0.7498 (t80) cc_final: 0.6333 (t80) REVERT: E 515 MET cc_start: 0.8905 (tpp) cc_final: 0.8345 (tpp) REVERT: E 553 LYS cc_start: 0.9342 (mttp) cc_final: 0.8609 (mttt) REVERT: E 624 THR cc_start: 0.9548 (p) cc_final: 0.9171 (t) REVERT: E 639 TYR cc_start: 0.8644 (m-80) cc_final: 0.8443 (m-80) REVERT: F 303 GLU cc_start: 0.6423 (mp0) cc_final: 0.5918 (mp0) REVERT: F 371 MET cc_start: 0.7232 (tmm) cc_final: 0.6883 (tmm) REVERT: F 473 MET cc_start: 0.6853 (tmm) cc_final: 0.6643 (tmm) REVERT: F 482 LEU cc_start: 0.9063 (mt) cc_final: 0.8828 (tt) REVERT: F 539 LEU cc_start: 0.9429 (tp) cc_final: 0.9056 (mp) REVERT: F 745 GLN cc_start: 0.8706 (mt0) cc_final: 0.8363 (mt0) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.3660 time to fit residues: 247.4741 Evaluate side-chains 324 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 178 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 326 optimal weight: 4.9990 chunk 313 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 269 optimal weight: 7.9990 chunk 295 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 585 GLN B 426 ASN B 459 HIS ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 785 ASN D 442 HIS E 459 HIS ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.097446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.076309 restraints weight = 69881.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.078471 restraints weight = 42328.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.079882 restraints weight = 29260.355| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27244 Z= 0.204 Angle : 0.611 8.512 36900 Z= 0.314 Chirality : 0.042 0.177 4196 Planarity : 0.005 0.054 4790 Dihedral : 10.093 88.911 4024 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.59 % Favored : 93.20 % Rotamer: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3397 helix: 1.27 (0.12), residues: 1812 sheet: -0.35 (0.27), residues: 357 loop : -0.82 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 219 HIS 0.007 0.001 HIS E 459 PHE 0.016 0.002 PHE A 731 TYR 0.035 0.002 TYR D 752 ARG 0.009 0.001 ARG D 361 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 1308) hydrogen bonds : angle 4.61570 ( 3753) covalent geometry : bond 0.00458 (27242) covalent geometry : angle 0.61088 (36900) Misc. bond : bond 0.00082 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 401 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LYS cc_start: 0.8710 (mmtp) cc_final: 0.8503 (ptmt) REVERT: A 546 CYS cc_start: 0.8845 (m) cc_final: 0.8516 (m) REVERT: A 566 ILE cc_start: 0.9632 (mm) cc_final: 0.9415 (mm) REVERT: B 240 LEU cc_start: 0.8546 (tp) cc_final: 0.7958 (tp) REVERT: B 302 ASP cc_start: 0.8326 (p0) cc_final: 0.7567 (p0) REVERT: B 305 ASP cc_start: 0.8974 (p0) cc_final: 0.8739 (p0) REVERT: B 395 ASN cc_start: 0.9192 (t0) cc_final: 0.8936 (t0) REVERT: B 401 LYS cc_start: 0.9213 (mttt) cc_final: 0.8880 (tppt) REVERT: B 546 CYS cc_start: 0.8800 (m) cc_final: 0.8383 (m) REVERT: B 740 MET cc_start: 0.8763 (tmm) cc_final: 0.8428 (tmm) REVERT: C 318 MET cc_start: 0.8700 (tmm) cc_final: 0.8337 (tmm) REVERT: C 327 MET cc_start: 0.9246 (tpp) cc_final: 0.9026 (tpp) REVERT: C 369 MET cc_start: 0.8657 (ptm) cc_final: 0.8398 (ptt) REVERT: C 473 MET cc_start: 0.7617 (tpt) cc_final: 0.7306 (tpp) REVERT: C 525 GLU cc_start: 0.8161 (pm20) cc_final: 0.7389 (mt-10) REVERT: C 574 LYS cc_start: 0.8945 (ptmt) cc_final: 0.8672 (ptmt) REVERT: C 596 CYS cc_start: 0.8750 (t) cc_final: 0.8332 (p) REVERT: C 649 MET cc_start: 0.7459 (mmt) cc_final: 0.7184 (mmm) REVERT: C 741 GLN cc_start: 0.8331 (tp40) cc_final: 0.7948 (tp-100) REVERT: D 204 ILE cc_start: 0.9176 (tt) cc_final: 0.8954 (pt) REVERT: D 281 GLU cc_start: 0.9074 (mp0) cc_final: 0.8712 (mp0) REVERT: D 466 TRP cc_start: 0.6838 (p90) cc_final: 0.6414 (p90) REVERT: D 580 GLU cc_start: 0.8853 (mp0) cc_final: 0.8409 (mp0) REVERT: D 649 MET cc_start: 0.8235 (tpt) cc_final: 0.7974 (tpp) REVERT: D 659 ARG cc_start: 0.8701 (mtt-85) cc_final: 0.8284 (mtt-85) REVERT: E 515 MET cc_start: 0.9001 (tpp) cc_final: 0.8396 (tpp) REVERT: E 624 THR cc_start: 0.9548 (p) cc_final: 0.9347 (t) REVERT: E 628 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8609 (mm-30) REVERT: F 303 GLU cc_start: 0.6465 (mp0) cc_final: 0.5886 (mp0) REVERT: F 371 MET cc_start: 0.7283 (tmm) cc_final: 0.6863 (tmm) REVERT: F 473 MET cc_start: 0.6739 (tmm) cc_final: 0.6529 (tmm) REVERT: F 603 MET cc_start: 0.8128 (tpp) cc_final: 0.7752 (tpp) REVERT: F 745 GLN cc_start: 0.8732 (mt0) cc_final: 0.8271 (mt0) outliers start: 2 outliers final: 1 residues processed: 403 average time/residue: 0.4032 time to fit residues: 265.7353 Evaluate side-chains 302 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 227 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 329 optimal weight: 0.0070 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 412 GLN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 ASN E 438 HIS ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.077743 restraints weight = 70475.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.079834 restraints weight = 43247.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.081272 restraints weight = 30178.945| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27244 Z= 0.145 Angle : 0.564 9.158 36900 Z= 0.288 Chirality : 0.042 0.155 4196 Planarity : 0.004 0.077 4790 Dihedral : 9.853 81.369 4024 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.92 % Favored : 93.85 % Rotamer: Outliers : 0.11 % Allowed : 2.64 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3397 helix: 1.34 (0.12), residues: 1809 sheet: -0.30 (0.27), residues: 364 loop : -0.78 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 780 HIS 0.006 0.001 HIS B 459 PHE 0.018 0.002 PHE D 587 TYR 0.035 0.001 TYR D 752 ARG 0.007 0.000 ARG C 589 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 1308) hydrogen bonds : angle 4.41198 ( 3753) covalent geometry : bond 0.00330 (27242) covalent geometry : angle 0.56405 (36900) Misc. bond : bond 0.00060 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 408 time to evaluate : 3.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASP cc_start: 0.8658 (m-30) cc_final: 0.8025 (p0) REVERT: A 522 LYS cc_start: 0.8733 (mmtp) cc_final: 0.8530 (ptpt) REVERT: A 546 CYS cc_start: 0.8816 (m) cc_final: 0.8488 (m) REVERT: B 240 LEU cc_start: 0.8552 (tp) cc_final: 0.7917 (tp) REVERT: B 302 ASP cc_start: 0.7906 (p0) cc_final: 0.7557 (p0) REVERT: B 303 GLU cc_start: 0.8276 (mp0) cc_final: 0.8029 (mp0) REVERT: B 305 ASP cc_start: 0.8905 (p0) cc_final: 0.8678 (p0) REVERT: B 395 ASN cc_start: 0.9174 (t0) cc_final: 0.8917 (t0) REVERT: B 401 LYS cc_start: 0.9164 (mttt) cc_final: 0.8827 (tppt) REVERT: B 546 CYS cc_start: 0.8786 (m) cc_final: 0.8341 (m) REVERT: B 603 MET cc_start: 0.8152 (mmt) cc_final: 0.7832 (mmp) REVERT: B 620 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7696 (ptp-170) REVERT: B 740 MET cc_start: 0.8772 (tmm) cc_final: 0.8367 (tmm) REVERT: B 797 TYR cc_start: 0.7539 (m-80) cc_final: 0.6892 (m-80) REVERT: C 318 MET cc_start: 0.8647 (tmm) cc_final: 0.8245 (tmm) REVERT: C 327 MET cc_start: 0.9210 (tpp) cc_final: 0.8995 (tpp) REVERT: C 369 MET cc_start: 0.8692 (ptm) cc_final: 0.8488 (ptt) REVERT: C 473 MET cc_start: 0.7589 (tpt) cc_final: 0.7357 (tpp) REVERT: C 493 SER cc_start: 0.9191 (m) cc_final: 0.8869 (p) REVERT: C 652 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7635 (pt0) REVERT: C 741 GLN cc_start: 0.8313 (tp40) cc_final: 0.7919 (tp40) REVERT: D 204 ILE cc_start: 0.9099 (tt) cc_final: 0.8848 (pt) REVERT: D 281 GLU cc_start: 0.9061 (mp0) cc_final: 0.8663 (mp0) REVERT: D 466 TRP cc_start: 0.6745 (p90) cc_final: 0.6156 (p90) REVERT: D 580 GLU cc_start: 0.8845 (mp0) cc_final: 0.8268 (mp0) REVERT: D 649 MET cc_start: 0.8264 (tpt) cc_final: 0.7990 (tpp) REVERT: D 659 ARG cc_start: 0.8632 (mtt-85) cc_final: 0.8351 (mtt-85) REVERT: D 740 MET cc_start: 0.7736 (tmm) cc_final: 0.7396 (tmm) REVERT: E 515 MET cc_start: 0.9016 (tpp) cc_final: 0.8435 (tpp) REVERT: E 603 MET cc_start: 0.9016 (mmt) cc_final: 0.8788 (mmp) REVERT: E 624 THR cc_start: 0.9543 (p) cc_final: 0.9342 (t) REVERT: E 628 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8437 (mm-30) REVERT: F 303 GLU cc_start: 0.6389 (mp0) cc_final: 0.5850 (mp0) REVERT: F 371 MET cc_start: 0.7463 (tmm) cc_final: 0.7077 (tmm) REVERT: F 603 MET cc_start: 0.8233 (tpp) cc_final: 0.7918 (tpp) outliers start: 3 outliers final: 0 residues processed: 411 average time/residue: 0.3620 time to fit residues: 244.0554 Evaluate side-chains 306 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 181 optimal weight: 4.9990 chunk 311 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 272 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 286 optimal weight: 20.0000 chunk 37 optimal weight: 0.6980 chunk 158 optimal weight: 7.9990 chunk 177 optimal weight: 0.0030 overall best weight: 2.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN B 459 HIS ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 GLN C 745 GLN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.077954 restraints weight = 69960.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.080062 restraints weight = 42622.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.081505 restraints weight = 29698.730| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27244 Z= 0.136 Angle : 0.560 9.836 36900 Z= 0.284 Chirality : 0.041 0.159 4196 Planarity : 0.004 0.070 4790 Dihedral : 9.688 77.485 4024 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.21 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3397 helix: 1.40 (0.12), residues: 1814 sheet: -0.34 (0.27), residues: 358 loop : -0.79 (0.19), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 219 HIS 0.003 0.001 HIS F 438 PHE 0.015 0.002 PHE D 731 TYR 0.037 0.001 TYR D 752 ARG 0.008 0.000 ARG D 351 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 1308) hydrogen bonds : angle 4.32036 ( 3753) covalent geometry : bond 0.00313 (27242) covalent geometry : angle 0.56015 (36900) Misc. bond : bond 0.00038 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASP cc_start: 0.8711 (m-30) cc_final: 0.8061 (p0) REVERT: A 546 CYS cc_start: 0.8753 (m) cc_final: 0.8444 (m) REVERT: B 240 LEU cc_start: 0.8595 (tp) cc_final: 0.7923 (tp) REVERT: B 302 ASP cc_start: 0.7931 (p0) cc_final: 0.7355 (p0) REVERT: B 303 GLU cc_start: 0.8313 (mp0) cc_final: 0.7899 (mp0) REVERT: B 305 ASP cc_start: 0.8890 (p0) cc_final: 0.8652 (p0) REVERT: B 401 LYS cc_start: 0.9195 (mttt) cc_final: 0.8828 (tppt) REVERT: B 546 CYS cc_start: 0.8768 (m) cc_final: 0.8323 (m) REVERT: B 603 MET cc_start: 0.8215 (mmt) cc_final: 0.7993 (mmp) REVERT: B 740 MET cc_start: 0.8786 (tmm) cc_final: 0.8370 (tmm) REVERT: B 797 TYR cc_start: 0.7555 (m-80) cc_final: 0.6974 (m-80) REVERT: C 318 MET cc_start: 0.8630 (tmm) cc_final: 0.8204 (tmm) REVERT: C 369 MET cc_start: 0.8635 (ptm) cc_final: 0.8402 (ptt) REVERT: C 452 ASP cc_start: 0.7315 (m-30) cc_final: 0.7105 (m-30) REVERT: C 473 MET cc_start: 0.7596 (tpt) cc_final: 0.7384 (tpp) REVERT: C 493 SER cc_start: 0.9191 (m) cc_final: 0.8873 (p) REVERT: C 525 GLU cc_start: 0.8089 (pm20) cc_final: 0.7267 (mt-10) REVERT: C 652 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7616 (pt0) REVERT: C 741 GLN cc_start: 0.8286 (tp-100) cc_final: 0.7954 (tp40) REVERT: D 204 ILE cc_start: 0.9109 (tt) cc_final: 0.8865 (pt) REVERT: D 281 GLU cc_start: 0.9045 (mp0) cc_final: 0.8578 (mp0) REVERT: D 286 ASP cc_start: 0.7900 (t70) cc_final: 0.7695 (t0) REVERT: D 398 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8507 (mm-30) REVERT: D 466 TRP cc_start: 0.6745 (p90) cc_final: 0.5968 (p90) REVERT: D 649 MET cc_start: 0.8267 (tpt) cc_final: 0.7986 (tpp) REVERT: D 659 ARG cc_start: 0.8630 (mtt-85) cc_final: 0.8397 (mtt-85) REVERT: D 740 MET cc_start: 0.7757 (tmm) cc_final: 0.7541 (tmm) REVERT: E 515 MET cc_start: 0.9001 (tpp) cc_final: 0.8430 (tpp) REVERT: E 624 THR cc_start: 0.9531 (p) cc_final: 0.9315 (t) REVERT: E 628 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8412 (mm-30) REVERT: F 219 TRP cc_start: 0.5932 (t-100) cc_final: 0.5693 (t-100) REVERT: F 303 GLU cc_start: 0.6378 (mp0) cc_final: 0.5831 (mp0) REVERT: F 318 MET cc_start: 0.4884 (mmt) cc_final: 0.4613 (mmt) REVERT: F 371 MET cc_start: 0.7473 (tmm) cc_final: 0.6822 (mmt) REVERT: F 585 GLN cc_start: 0.8677 (tt0) cc_final: 0.8465 (tp40) REVERT: F 603 MET cc_start: 0.8241 (tpp) cc_final: 0.7829 (tpp) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.4892 time to fit residues: 333.9853 Evaluate side-chains 303 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 4.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 108 optimal weight: 6.9990 chunk 319 optimal weight: 3.9990 chunk 305 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 317 optimal weight: 0.0470 chunk 75 optimal weight: 0.8980 chunk 265 optimal weight: 0.8980 chunk 129 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 81 optimal weight: 0.0470 chunk 148 optimal weight: 4.9990 overall best weight: 1.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 328 ASN C 412 GLN C 426 ASN E 438 HIS ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.100495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.079357 restraints weight = 69585.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.081482 restraints weight = 42311.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.082943 restraints weight = 29486.978| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27244 Z= 0.109 Angle : 0.550 12.539 36900 Z= 0.277 Chirality : 0.041 0.263 4196 Planarity : 0.004 0.079 4790 Dihedral : 9.499 75.863 4024 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.50 % Favored : 94.26 % Rotamer: Outliers : 0.07 % Allowed : 1.94 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 3397 helix: 1.53 (0.12), residues: 1811 sheet: -0.32 (0.27), residues: 360 loop : -0.71 (0.19), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 453 HIS 0.007 0.001 HIS E 438 PHE 0.022 0.001 PHE A 731 TYR 0.038 0.001 TYR D 752 ARG 0.008 0.000 ARG D 361 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 1308) hydrogen bonds : angle 4.19671 ( 3753) covalent geometry : bond 0.00247 (27242) covalent geometry : angle 0.55001 (36900) Misc. bond : bond 0.00006 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 408 time to evaluate : 5.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASP cc_start: 0.8743 (m-30) cc_final: 0.8121 (p0) REVERT: A 546 CYS cc_start: 0.8670 (m) cc_final: 0.8318 (m) REVERT: A 652 GLU cc_start: 0.7583 (mp0) cc_final: 0.7375 (mp0) REVERT: A 772 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7474 (mp0) REVERT: B 240 LEU cc_start: 0.8452 (tp) cc_final: 0.7907 (tp) REVERT: B 303 GLU cc_start: 0.8376 (mp0) cc_final: 0.7922 (mp0) REVERT: B 305 ASP cc_start: 0.8836 (p0) cc_final: 0.8562 (p0) REVERT: B 319 GLU cc_start: 0.7943 (pm20) cc_final: 0.7736 (pm20) REVERT: B 401 LYS cc_start: 0.9163 (mttt) cc_final: 0.8813 (tppt) REVERT: B 546 CYS cc_start: 0.8730 (m) cc_final: 0.8250 (m) REVERT: B 740 MET cc_start: 0.8751 (tmm) cc_final: 0.8295 (tmm) REVERT: C 318 MET cc_start: 0.8619 (tmm) cc_final: 0.8153 (tmm) REVERT: C 369 MET cc_start: 0.8678 (ptm) cc_final: 0.8465 (ptt) REVERT: C 493 SER cc_start: 0.9156 (m) cc_final: 0.8845 (p) REVERT: C 525 GLU cc_start: 0.8051 (pm20) cc_final: 0.7288 (mt-10) REVERT: C 574 LYS cc_start: 0.8954 (ptmt) cc_final: 0.8652 (ptmt) REVERT: D 204 ILE cc_start: 0.9072 (tt) cc_final: 0.8804 (pt) REVERT: D 272 VAL cc_start: 0.9395 (m) cc_final: 0.9122 (p) REVERT: D 281 GLU cc_start: 0.9035 (mp0) cc_final: 0.8547 (mp0) REVERT: D 398 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8370 (mm-30) REVERT: D 466 TRP cc_start: 0.6570 (p90) cc_final: 0.6007 (p90) REVERT: D 473 MET cc_start: 0.8350 (mmm) cc_final: 0.7979 (mmm) REVERT: D 649 MET cc_start: 0.8222 (tpt) cc_final: 0.7952 (tpp) REVERT: D 659 ARG cc_start: 0.8613 (mtt-85) cc_final: 0.8360 (mtt-85) REVERT: D 740 MET cc_start: 0.7813 (tmm) cc_final: 0.7575 (tmm) REVERT: E 515 MET cc_start: 0.9040 (tpp) cc_final: 0.8518 (tpp) REVERT: E 550 LEU cc_start: 0.8567 (mt) cc_final: 0.8033 (mt) REVERT: E 553 LYS cc_start: 0.9336 (mttp) cc_final: 0.8720 (mttt) REVERT: E 624 THR cc_start: 0.9526 (p) cc_final: 0.9313 (t) REVERT: E 628 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8329 (mm-30) REVERT: F 219 TRP cc_start: 0.5955 (t-100) cc_final: 0.5644 (t-100) REVERT: F 303 GLU cc_start: 0.6363 (mp0) cc_final: 0.5822 (mp0) REVERT: F 318 MET cc_start: 0.4754 (mmt) cc_final: 0.4483 (mmt) REVERT: F 371 MET cc_start: 0.7420 (tmm) cc_final: 0.7140 (tmm) REVERT: F 603 MET cc_start: 0.8211 (tpp) cc_final: 0.7789 (tpp) REVERT: F 649 MET cc_start: 0.8089 (mpp) cc_final: 0.7823 (mpp) outliers start: 2 outliers final: 0 residues processed: 410 average time/residue: 0.4879 time to fit residues: 331.3154 Evaluate side-chains 306 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 5.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 96 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 56 optimal weight: 0.1980 chunk 236 optimal weight: 20.0000 chunk 92 optimal weight: 0.0570 chunk 337 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 324 optimal weight: 8.9990 chunk 177 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 overall best weight: 2.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 426 ASN B 459 HIS C 328 ASN C 426 ASN C 738 ASN ** C 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 GLN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS F 484 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.099058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.078149 restraints weight = 70148.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.080147 restraints weight = 43226.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.081558 restraints weight = 30505.871| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27244 Z= 0.148 Angle : 0.581 10.401 36900 Z= 0.294 Chirality : 0.042 0.183 4196 Planarity : 0.004 0.082 4790 Dihedral : 9.466 76.565 4024 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.56 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3397 helix: 1.52 (0.12), residues: 1806 sheet: -0.32 (0.27), residues: 358 loop : -0.73 (0.19), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 453 HIS 0.005 0.001 HIS F 438 PHE 0.016 0.002 PHE B 264 TYR 0.036 0.001 TYR D 752 ARG 0.008 0.000 ARG D 361 Details of bonding type rmsd hydrogen bonds : bond 0.03196 ( 1308) hydrogen bonds : angle 4.25847 ( 3753) covalent geometry : bond 0.00339 (27242) covalent geometry : angle 0.58084 (36900) Misc. bond : bond 0.00051 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASP cc_start: 0.8744 (m-30) cc_final: 0.8133 (p0) REVERT: A 406 TYR cc_start: 0.8802 (m-80) cc_final: 0.8599 (m-80) REVERT: A 546 CYS cc_start: 0.8661 (m) cc_final: 0.8330 (m) REVERT: A 772 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7449 (mm-30) REVERT: B 240 LEU cc_start: 0.8509 (tp) cc_final: 0.7946 (tp) REVERT: B 305 ASP cc_start: 0.8866 (p0) cc_final: 0.8568 (p0) REVERT: B 319 GLU cc_start: 0.8018 (pm20) cc_final: 0.7806 (pm20) REVERT: B 401 LYS cc_start: 0.9189 (mttt) cc_final: 0.8818 (tppt) REVERT: B 546 CYS cc_start: 0.8733 (m) cc_final: 0.8294 (m) REVERT: B 740 MET cc_start: 0.8766 (tmm) cc_final: 0.8363 (tmm) REVERT: B 797 TYR cc_start: 0.7542 (m-80) cc_final: 0.6610 (m-80) REVERT: C 318 MET cc_start: 0.8652 (tmm) cc_final: 0.8136 (tmm) REVERT: C 369 MET cc_start: 0.8638 (ptm) cc_final: 0.8385 (ptt) REVERT: C 493 SER cc_start: 0.9184 (m) cc_final: 0.8868 (p) REVERT: C 574 LYS cc_start: 0.8956 (ptmt) cc_final: 0.8658 (ptmt) REVERT: C 646 ARG cc_start: 0.8629 (ptt90) cc_final: 0.8376 (ptt90) REVERT: D 231 MET cc_start: 0.6401 (mmm) cc_final: 0.5985 (tpt) REVERT: D 398 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8395 (mm-30) REVERT: D 466 TRP cc_start: 0.6739 (p90) cc_final: 0.5946 (p90) REVERT: D 649 MET cc_start: 0.8241 (tpt) cc_final: 0.7966 (tpp) REVERT: D 740 MET cc_start: 0.7784 (tmm) cc_final: 0.7545 (tmm) REVERT: E 515 MET cc_start: 0.9045 (tpp) cc_final: 0.8500 (tpp) REVERT: E 603 MET cc_start: 0.9051 (mmt) cc_final: 0.8844 (mmp) REVERT: E 624 THR cc_start: 0.9544 (p) cc_final: 0.9314 (t) REVERT: E 628 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8380 (mm-30) REVERT: F 219 TRP cc_start: 0.5899 (t-100) cc_final: 0.5553 (t-100) REVERT: F 303 GLU cc_start: 0.6401 (mp0) cc_final: 0.5877 (mp0) REVERT: F 369 MET cc_start: 0.2876 (mpp) cc_final: 0.2511 (mpp) REVERT: F 371 MET cc_start: 0.7500 (tmm) cc_final: 0.7194 (tmm) REVERT: F 603 MET cc_start: 0.8173 (tpp) cc_final: 0.7729 (tpp) REVERT: F 649 MET cc_start: 0.8230 (mpp) cc_final: 0.7977 (mpp) REVERT: F 745 GLN cc_start: 0.8622 (mt0) cc_final: 0.8228 (mt0) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.3396 time to fit residues: 223.1669 Evaluate side-chains 300 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 90 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 322 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 295 optimal weight: 20.0000 chunk 163 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN B 459 HIS B 623 ASN C 328 ASN C 426 ASN C 738 ASN ** C 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.097943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.077008 restraints weight = 70666.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.079030 restraints weight = 43801.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.080422 restraints weight = 30769.248| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27244 Z= 0.186 Angle : 0.617 10.631 36900 Z= 0.313 Chirality : 0.043 0.195 4196 Planarity : 0.005 0.095 4790 Dihedral : 9.554 75.455 4024 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.62 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3397 helix: 1.39 (0.12), residues: 1821 sheet: -0.29 (0.27), residues: 355 loop : -0.82 (0.19), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 453 HIS 0.008 0.001 HIS F 438 PHE 0.031 0.002 PHE D 354 TYR 0.034 0.002 TYR D 752 ARG 0.010 0.000 ARG D 361 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 1308) hydrogen bonds : angle 4.36481 ( 3753) covalent geometry : bond 0.00423 (27242) covalent geometry : angle 0.61747 (36900) Misc. bond : bond 0.00084 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 3.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8839 (tp30) REVERT: A 286 ASP cc_start: 0.8705 (m-30) cc_final: 0.8154 (p0) REVERT: A 546 CYS cc_start: 0.8683 (m) cc_final: 0.8369 (m) REVERT: B 240 LEU cc_start: 0.8522 (tp) cc_final: 0.7939 (tp) REVERT: B 305 ASP cc_start: 0.8913 (p0) cc_final: 0.8632 (p0) REVERT: B 319 GLU cc_start: 0.8020 (pm20) cc_final: 0.7781 (pm20) REVERT: B 401 LYS cc_start: 0.9167 (mttt) cc_final: 0.8832 (tppt) REVERT: B 546 CYS cc_start: 0.8787 (m) cc_final: 0.8300 (m) REVERT: B 740 MET cc_start: 0.8788 (tmm) cc_final: 0.8535 (tmm) REVERT: C 318 MET cc_start: 0.8718 (tmm) cc_final: 0.8200 (tmm) REVERT: C 369 MET cc_start: 0.8622 (ptm) cc_final: 0.8399 (ptt) REVERT: C 493 SER cc_start: 0.9200 (m) cc_final: 0.8900 (p) REVERT: C 525 GLU cc_start: 0.8163 (pm20) cc_final: 0.7182 (mt-10) REVERT: C 574 LYS cc_start: 0.8970 (ptmt) cc_final: 0.8669 (ptmt) REVERT: C 646 ARG cc_start: 0.8738 (ptt90) cc_final: 0.8489 (ptt90) REVERT: D 204 ILE cc_start: 0.9098 (tt) cc_final: 0.8887 (pt) REVERT: D 231 MET cc_start: 0.6403 (mmm) cc_final: 0.5978 (tpt) REVERT: D 466 TRP cc_start: 0.6896 (p90) cc_final: 0.5881 (p90) REVERT: D 546 CYS cc_start: 0.8430 (m) cc_final: 0.8030 (m) REVERT: D 550 LEU cc_start: 0.8800 (pp) cc_final: 0.8549 (tp) REVERT: D 649 MET cc_start: 0.8301 (tpt) cc_final: 0.8047 (tpp) REVERT: D 740 MET cc_start: 0.7828 (tmm) cc_final: 0.7558 (tmm) REVERT: E 515 MET cc_start: 0.9038 (tpp) cc_final: 0.8490 (tpp) REVERT: E 603 MET cc_start: 0.9223 (mmt) cc_final: 0.9012 (mmp) REVERT: E 624 THR cc_start: 0.9551 (p) cc_final: 0.9308 (t) REVERT: E 626 LEU cc_start: 0.8874 (mm) cc_final: 0.8347 (mm) REVERT: E 628 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8424 (mm-30) REVERT: F 303 GLU cc_start: 0.6427 (mp0) cc_final: 0.5888 (mp0) REVERT: F 367 ILE cc_start: 0.7142 (mt) cc_final: 0.6871 (mt) REVERT: F 369 MET cc_start: 0.2781 (mpp) cc_final: 0.2356 (mpp) REVERT: F 371 MET cc_start: 0.7525 (tmm) cc_final: 0.7267 (tmm) REVERT: F 603 MET cc_start: 0.8255 (tpp) cc_final: 0.8022 (tpp) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.3683 time to fit residues: 236.2232 Evaluate side-chains 303 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 167 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 334 optimal weight: 20.0000 chunk 276 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 239 optimal weight: 2.9990 chunk 341 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 333 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 ASN B 426 ASN B 623 ASN C 328 ASN C 426 ASN C 738 ASN ** C 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.097050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.076031 restraints weight = 70971.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.078069 restraints weight = 44226.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.079431 restraints weight = 31114.064| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 27244 Z= 0.202 Angle : 0.639 10.683 36900 Z= 0.323 Chirality : 0.043 0.210 4196 Planarity : 0.005 0.109 4790 Dihedral : 9.682 79.995 4024 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.95 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 3397 helix: 1.37 (0.12), residues: 1804 sheet: -0.32 (0.28), residues: 355 loop : -0.83 (0.19), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 219 HIS 0.007 0.001 HIS F 438 PHE 0.023 0.002 PHE B 476 TYR 0.031 0.002 TYR D 752 ARG 0.017 0.000 ARG B 360 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 1308) hydrogen bonds : angle 4.46275 ( 3753) covalent geometry : bond 0.00460 (27242) covalent geometry : angle 0.63851 (36900) Misc. bond : bond 0.00108 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8849 (tp30) REVERT: A 546 CYS cc_start: 0.8731 (m) cc_final: 0.8427 (m) REVERT: B 240 LEU cc_start: 0.8604 (tp) cc_final: 0.7939 (tp) REVERT: B 305 ASP cc_start: 0.8940 (p0) cc_final: 0.8713 (p0) REVERT: B 319 GLU cc_start: 0.8031 (pm20) cc_final: 0.7792 (pm20) REVERT: B 368 ASP cc_start: 0.8243 (p0) cc_final: 0.7916 (p0) REVERT: B 401 LYS cc_start: 0.9204 (mttt) cc_final: 0.8846 (tppt) REVERT: B 546 CYS cc_start: 0.8858 (m) cc_final: 0.8386 (m) REVERT: B 603 MET cc_start: 0.8124 (mmp) cc_final: 0.7899 (mmp) REVERT: B 731 PHE cc_start: 0.8172 (m-80) cc_final: 0.7968 (m-80) REVERT: B 740 MET cc_start: 0.8825 (tmm) cc_final: 0.8418 (tmm) REVERT: B 797 TYR cc_start: 0.7357 (m-80) cc_final: 0.7122 (m-80) REVERT: C 318 MET cc_start: 0.8714 (tmm) cc_final: 0.8238 (tmm) REVERT: C 369 MET cc_start: 0.8574 (ptm) cc_final: 0.8303 (ptt) REVERT: C 473 MET cc_start: 0.7140 (tpp) cc_final: 0.6887 (tpp) REVERT: C 493 SER cc_start: 0.9178 (m) cc_final: 0.8895 (p) REVERT: C 525 GLU cc_start: 0.8242 (pm20) cc_final: 0.7093 (mt-10) REVERT: C 574 LYS cc_start: 0.8971 (ptmt) cc_final: 0.8659 (ptmt) REVERT: D 286 ASP cc_start: 0.7914 (t70) cc_final: 0.7682 (t0) REVERT: D 402 MET cc_start: 0.8806 (mtm) cc_final: 0.8577 (mtm) REVERT: D 546 CYS cc_start: 0.8435 (m) cc_final: 0.8033 (m) REVERT: D 550 LEU cc_start: 0.8821 (pp) cc_final: 0.8574 (tp) REVERT: D 649 MET cc_start: 0.8273 (tpt) cc_final: 0.7993 (tpp) REVERT: D 740 MET cc_start: 0.7831 (tmm) cc_final: 0.7561 (tmm) REVERT: E 515 MET cc_start: 0.9042 (tpp) cc_final: 0.8482 (tpp) REVERT: E 603 MET cc_start: 0.9223 (mmt) cc_final: 0.9006 (mmp) REVERT: E 624 THR cc_start: 0.9534 (p) cc_final: 0.9286 (t) REVERT: E 628 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8427 (mm-30) REVERT: F 219 TRP cc_start: 0.6066 (t-100) cc_final: 0.5664 (t-100) REVERT: F 367 ILE cc_start: 0.7205 (mt) cc_final: 0.6945 (mt) REVERT: F 369 MET cc_start: 0.2783 (mpp) cc_final: 0.2421 (mpp) REVERT: F 371 MET cc_start: 0.7536 (tmm) cc_final: 0.7292 (tmm) REVERT: F 539 LEU cc_start: 0.9169 (tt) cc_final: 0.8898 (mp) REVERT: F 603 MET cc_start: 0.8259 (tpp) cc_final: 0.8013 (tpp) REVERT: F 649 MET cc_start: 0.8213 (mpp) cc_final: 0.7964 (mpp) REVERT: F 745 GLN cc_start: 0.8563 (mt0) cc_final: 0.8206 (mt0) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.3927 time to fit residues: 251.2204 Evaluate side-chains 304 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 129 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 283 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 271 optimal weight: 7.9990 chunk 336 optimal weight: 20.0000 chunk 190 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 337 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 328 ASN C 426 ASN C 738 ASN ** C 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.098209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.077325 restraints weight = 69918.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.079386 restraints weight = 43120.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.080723 restraints weight = 30188.891| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27244 Z= 0.149 Angle : 0.608 11.631 36900 Z= 0.306 Chirality : 0.042 0.183 4196 Planarity : 0.005 0.100 4790 Dihedral : 9.591 82.621 4024 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.33 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3397 helix: 1.42 (0.12), residues: 1796 sheet: -0.35 (0.27), residues: 356 loop : -0.87 (0.19), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 453 HIS 0.005 0.001 HIS F 438 PHE 0.015 0.002 PHE B 264 TYR 0.033 0.001 TYR D 752 ARG 0.008 0.000 ARG D 361 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 1308) hydrogen bonds : angle 4.33782 ( 3753) covalent geometry : bond 0.00344 (27242) covalent geometry : angle 0.60824 (36900) Misc. bond : bond 0.00050 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.5492 (tpt) cc_final: 0.4983 (tpp) REVERT: A 546 CYS cc_start: 0.8732 (m) cc_final: 0.8359 (m) REVERT: A 772 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7275 (mp0) REVERT: B 240 LEU cc_start: 0.8562 (tp) cc_final: 0.7949 (tp) REVERT: B 305 ASP cc_start: 0.8891 (p0) cc_final: 0.8654 (p0) REVERT: B 319 GLU cc_start: 0.8017 (pm20) cc_final: 0.7794 (pm20) REVERT: B 368 ASP cc_start: 0.8216 (p0) cc_final: 0.7910 (p0) REVERT: B 401 LYS cc_start: 0.9169 (mttt) cc_final: 0.8816 (tppt) REVERT: B 546 CYS cc_start: 0.8819 (m) cc_final: 0.8320 (m) REVERT: B 740 MET cc_start: 0.8779 (tmm) cc_final: 0.8330 (tmm) REVERT: B 797 TYR cc_start: 0.7312 (m-80) cc_final: 0.7004 (m-80) REVERT: C 318 MET cc_start: 0.8678 (tmm) cc_final: 0.8176 (tmm) REVERT: C 369 MET cc_start: 0.8621 (ptm) cc_final: 0.8394 (ptt) REVERT: C 493 SER cc_start: 0.9162 (m) cc_final: 0.8847 (p) REVERT: C 525 GLU cc_start: 0.8166 (pm20) cc_final: 0.7191 (mt-10) REVERT: C 574 LYS cc_start: 0.8968 (ptmt) cc_final: 0.8652 (ptmt) REVERT: D 286 ASP cc_start: 0.7839 (t70) cc_final: 0.7600 (t0) REVERT: D 466 TRP cc_start: 0.7060 (p90) cc_final: 0.6016 (p90) REVERT: D 546 CYS cc_start: 0.8386 (m) cc_final: 0.8177 (m) REVERT: D 649 MET cc_start: 0.8264 (tpt) cc_final: 0.8007 (tpp) REVERT: D 740 MET cc_start: 0.7813 (tmm) cc_final: 0.7513 (tmm) REVERT: E 304 ILE cc_start: 0.9258 (tp) cc_final: 0.9054 (tp) REVERT: E 515 MET cc_start: 0.9033 (tpp) cc_final: 0.8485 (tpp) REVERT: E 603 MET cc_start: 0.9138 (mmt) cc_final: 0.8929 (mmp) REVERT: E 624 THR cc_start: 0.9544 (p) cc_final: 0.9287 (t) REVERT: E 628 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8405 (mm-30) REVERT: F 219 TRP cc_start: 0.5924 (t-100) cc_final: 0.5656 (t-100) REVERT: F 303 GLU cc_start: 0.6530 (mp0) cc_final: 0.6036 (mp0) REVERT: F 367 ILE cc_start: 0.7279 (mt) cc_final: 0.7015 (mt) REVERT: F 369 MET cc_start: 0.2677 (mpp) cc_final: 0.2286 (mpp) REVERT: F 371 MET cc_start: 0.7539 (tmm) cc_final: 0.7310 (tmm) REVERT: F 515 MET cc_start: 0.8592 (ppp) cc_final: 0.8037 (ppp) REVERT: F 539 LEU cc_start: 0.9139 (tt) cc_final: 0.8913 (mp) REVERT: F 603 MET cc_start: 0.8260 (tpp) cc_final: 0.7988 (tpp) REVERT: F 649 MET cc_start: 0.8262 (mpp) cc_final: 0.7975 (mpp) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.3624 time to fit residues: 234.8394 Evaluate side-chains 306 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 4.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 259 optimal weight: 7.9990 chunk 208 optimal weight: 0.0670 chunk 22 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 329 optimal weight: 5.9990 chunk 336 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 279 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN B 623 ASN C 328 ASN C 426 ASN C 738 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 745 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.097230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.076429 restraints weight = 70538.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.078419 restraints weight = 43310.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.079797 restraints weight = 30494.397| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27244 Z= 0.188 Angle : 0.632 11.117 36900 Z= 0.320 Chirality : 0.043 0.200 4196 Planarity : 0.005 0.088 4790 Dihedral : 9.649 85.719 4024 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.98 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 3397 helix: 1.36 (0.12), residues: 1797 sheet: -0.43 (0.28), residues: 338 loop : -0.91 (0.19), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 219 HIS 0.007 0.001 HIS F 438 PHE 0.026 0.002 PHE A 300 TYR 0.015 0.001 TYR D 752 ARG 0.009 0.000 ARG D 361 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 1308) hydrogen bonds : angle 4.40515 ( 3753) covalent geometry : bond 0.00430 (27242) covalent geometry : angle 0.63182 (36900) Misc. bond : bond 0.00062 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8708.49 seconds wall clock time: 160 minutes 14.43 seconds (9614.43 seconds total)